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Fudgy homemade brownie cupcakes with cookie dough frosting on top. One incredible dessert that you’ll want to make again and again!

brownie cupcakes with cookie dough frosting

There’s also nothing like finishing the day with dense fudgy brownies, cupcakes, and cookie dough.

overview photo of brownie cupcakes with cookie dough frosting

These fudge brownie cupcakes are so chocolatey that your head will spin. They aren’t light and fluffy like regular chocolate cupcakes, nor are they as dense as homemade brownies. But they are so rich, so moist, so fudgy, and will practically melt in your mouth. Eating one is by far, the best chocolate experience I’ve ever had. Yes, the brownie cupcakes themselves are an experience.

Now, let’s move on to the frosting. It’s like the dough from my favorite chocolate chip cookies, but smooth enough to slather onto a cupcake or a graham cracker or a pretzel (try it).

brownie cupcakes with cookie dough frosting

This egg-free cookie dough frosting is made with heat-treated flour. Raw flour can be a carrier of E. coli unless it goes through a heating process to kill the bacteria. (Think about it– flour is usually baked in a recipe.)

How to Heat Treat Flour

Option 1 – Microwave

  1. You can heat treat your entire bag of flour or just treat the amount you need in a single recipe. If you’re heating just enough for the recipe, add an extra 1/2 – 1 cup to be sure you have enough.
  2. Place the flour in a microwave-safe bowl and heat on high for 30 seconds at a time, stopping and stirring after each. Stir well to make sure none of the flour burns. Use an instant-read thermometer to test the flour in several places to make sure it has reached 165°F (74°C). If you get a lower reading in one area, stir and heat for an additional 30 seconds until it’s all ready.
  3. Measure the amount of flour you need and use in the recipe, then let it cool completely.

Option 2 – Oven

  1. Preheat oven to 300°F (149°C). Spread more flour than the recipe calls for on an un-greased rimmed baking pan, such as a 9×13 inch baking pan or 9×9 inch baking pan. Then follow a process similar to the microwave method by stirring and checking the temperature at 2 minute intervals. Be sure to check multiple spots of the flour to make sure it has all reached 165°F (74°C).
  2. If some flour sticks to the bottom or sides of the pan, don’t worry, just leave it there. You used more flour than needed in the recipe anyway. Don’t scrape it off because it will add small clumps to your batter/dough.
  3. If your flour is really clumpy, your oven might be too hot. Break it up with your fingers or pour all the flour into a bowl and whisk it. Discard any chunks if necessary.
  4. Measure the amount of flour you need and use in the recipe, then let it cool completely.

If you enjoy cookie dough inspired treats as much as I do, try this cookie dough fudge next. You’ll love it!

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brownie cupcakes with cookie dough frosting

Fudge Brownie Cupcakes with Cookie Dough Frosting

  • Author: Sally
  • Prep Time: 15 minutes
  • Cook Time: 22 minutes
  • Total Time: 2 hours
  • Yield: 12 cupcakes 1x
  • Category: Cupcakes
  • Method: Baking
  • Cuisine: American


Fudgy homemade brownie cupcakes with cookie dough frosting on top. One incredible dessert that you’ll want to make again and again!



Brownie Cupcakes

  • 4 ounces unsweetened or bittersweet chocolate, chopped (I used Ghirardelli)
  • 1/2 cup (115g) unsalted butter, cut into cubes
  • 1 and 1/4 cups (250g) granulated sugar
  • 1 teaspoon pure vanilla extract
  • 3 large eggs
  • 3/4 cup (94g) all-purpose flour (spoon & leveled)
  • 1/4 teaspoon salt

Cookie Dough Frosting

  • 1/2 cup (115g) unsalted butter, softened to room temperature
  • 3/4 cup (150g) packed light brown sugar
  • 1 teaspoon pure vanilla extract
  • 1 cup + 2 Tablespoons (140g) heat-treated all-purpose flour* (spoon & leveled)
  • 1/2 teaspoon salt
  • 1/4 cup (60ml) milk*
  • 1 cup (180g) mini chocolate chips


  1. Preheat oven to 325°F (163°C). Line 12 muffin tins with baking cups or spray with nonstick spray. Set aside.
  2. Make the brownie cupcakes: Melt the chopped chocolate and sliced butter together in the microwave in 30 second increments, stirring after each until completely smooth and combined. Allow to cool for a few minutes. Stir in sugar, then vanilla. Add in eggs, 1 at a time, mixing well after each addition. Mix in the flour and salt.
  3. Pour batter into 12 muffin tins and bake for 20-23 minutes. Mine took 22 minutes. A toothpick inserted in the center will have moist crumbs. Be careful not to overbake the cupcakes.
  4. Make the frosting: While the cupcakes are cooling in the pan, make the frosting. With an electric or stand mixer fitted with a paddle attachment, cream together the butter and sugar at medium speed. Add the vanilla and beat well. Stir in the flour and salt until doughy. Stir in the milk and beat until fluffy. Gently fold in chocolate chips. Frost cooled cupcakes.


  1. Heat Treated Flour: Though raw all-purpose flour is fine to use in the brownie cupcakes since you’re baking them, it’s safest to use heat-treated flour in the frosting. See note/instructions above recipe or purchase it online.
  2. Milk: I used vanilla almond milk, but any dairy or nondairy milk would be fine.
  3. Boxed Mix: You could easily use boxed brownie mix as a shortcut, but you would need to adjust the frosting accordingly since the cookie dough frosting recipe below only makes enough for 10-12 cupcakes.
  4. Tip: I find these cupcakes are best served cold. I keep mine in the refrigerator.

Keywords: fudge brownie cupcakes, fudge brownie cupcakes with cookie dough frosting

Reader Questions and Reviews

  1. How would subbing in cocoa powder for the baking chocolate turn out? Making these today, trying to avoid having to run to the store 🙂 

  2. Your recipes are amazing and I will be making many of your cupcakes for an upcoming bake sale.  I was wondering if I could make the cookie dough frosting…salted caramel frosting….and the vanilla and chocolate frosting used in the marble cupcakes ahead of time and just put them in my refrigerator?  I was thinking a day or two ahead of time so I’m not doing everything in one night.  


      1. Thank you for noting the frosting can be made in advance! I tend to over cook brownies. Do you have any pictures or tips to help me with this?

  3. Theses brownie cupcakes with cookie dough icing were amazing! My whole family loved them and my daughter asked if I could just make her extra cookie dough next time (I work in food safety so my kids have never had cookie dough with raw eggs and neither should you)! Another great recipe that even a beginner baker can make.

  4. Oh my GOSH!!! These were sooo insanely good!!! I took one bite and just about died. Thank you, Sally, for another INCREDIBLE recipe!!!

  5. My family and I love milk chocolate brownies I was wondering if you could use Milk Chocolate in these instead of unsweetened or bitter sweet chocolate? If I can is there anything else I need to do to the recipe? I have made your Chewy Fudge Homemade Brownies with Milk Chocolate they are absolutely amazing!!! My whole family and I LOVE them and any time I take them some where they are always the first to go! Every one always asks for the recipe! Of course I always tell them your website because you are the most amazing food blogger!!! Your recipes NEVER EVER disappoint!!! Thank you Sally!!!! 

  6. Hii…i was wondering if i can use this icing for a regular brownie batter which is baked in cupcake moulds??

  7. Made this for a potluck lunch at work the other day. Followed the recipe exactly, except I did mini cupcakes. They were a big hit! I made the cupcakes and frosted them the night before. It all came together pretty quickly. Refrigerated overnight, then left at room temp a few hours before serving. Perfect and delicious! (I did try one cold, but they were kind of hard and the cupcake stuck to the wrapper.) FYI – it made 36 mini cupcakes and just enough frosting; I will definitely make this one again. Thanks for the recipe!

  8. Thank you for this wonderful recipe! We teach Sunday School and I will usually bring a snack for the kids, and these have been a Big hit with both the high schoolers and jr. highers. In fact, when I mentioned bringing snacks into the Jr. High, one of the girls said, YES, my sisters told me about these brownie things you made with cookie dough on them! And after I brought them to the Jr. Highers for a snack I had one of their mom’s come up to me and ask for the recipe because her daughter Loved them! I do find that I need to bake them quite a bit longer than the recipe states, but since I live at over 7000 feet, I’m used to recipes being different. I love that the recipe is quick and easy and has such great results. Thanks again!

  9. I never leave comments on recipes, but this was absolutely the most amazing cupcake I have ever made! I love the combination of brownies and cookie dough, and not only was this recipe super simple and easy, but also absolutely delicious! If you love indulgent desserts- this one is for you!

  10. Hello! 
    If I’m baking these the night before I’m serving them, should I frost them the night before or just before serving them/closer to when I serve them?


  11. Hi! I’m making these for a coworkers’ birthday this week. I need them for Thursday. Can I make them tonight (Tuesday), and frost them tomorrow (Wednesday)? I want them to be their best, so if I need to do the whole process Wednesday, I can.

    Also, I’m going to make them into mini-cupcakes. What would you recommend for baking time? Thanks!

    1. Absolutely– I’d keep them at room temp overnight then in the fridge after you frost them. Mini bake time should probably be 10-13 minutes

  12. Good morning! Quick question about the frosting. Can it be piped onto the cupcakes, or is it not the right consistency for piping?

    1. Never mind! I just found the answer in a comment from 2 years ago. Apparently piping will work! 🙂

  13. Hi Sally! I made these before and they were amazing! I’m making them again for my husbands birthday but I can’t remember if I ended up using bittersweet or unsweetened chocolate. Which do you prefer?

  14. Hi 🙂 I was wondering if it would be possible to use dark chocolate instead of bittersweet or semi-sweet chocolate? Thank you x

  15. Is it okay to use semi sweet chocolate for the cupcakes, or would that be too sweet?
    I do have unsweetened chocolate, but not bittersweet. I am staying out of grocery stores until after Thanksgiving! Thanks!

  16. I am planning on making these in the morning! I am sure they will be a HUGE HIT in my house as my family loves “brookies” and this will put a frosty spin on the norm! Thanks so much for this recipe!!! 🙂 I can’t wait to try it!!!

  17. Hello Sally! I made this cookie dough frosting with your Simply Vanilla Cupcake recipe for a church event last night and to celebrate the essence of National Chocolate Chip Cookie Day! Those mini cupcakes were devoured! Thank you for your amazing, moist, and delish recipes!!!

    1. These are the most amazing cupcakes I’ve ever tasted!!!
      Thank you for this recipe Sally!!

  18. Could I freeze these brownie cupcakes like I do my regular cupcakes , when baking in advance ?

  19. Is the frosting recipe for 12 brownie cupcakes? I need to make enough icing to cover 50 cupcakes and am therefore doing 4x the brownie recipe but, how many times should I multiply the recipe by for the cooking dough frosting?
    By the way this recipe is a hit in my family!

    1. Hi Shauna, correct, this frosting is enough for 12 cupcakes, so you can scale it accordingly for the 50 cupcakes. So glad this recipe is a favorite for your family!

  20. So yummy! My brownies made a cave as soon as i took them out of the oven but everything was so good.

  21. These are fantastic! My son and I make them over and over again. If I want to make them into mini cupcakes for Thanksgiving, how long would you suggest baking them?

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